Table_2_Microbial Community Analysis and Food Safety Practice Survey-Based Hazard Identification and Risk Assessment for Controlled Environment Hydroponic/Aquaponic Farming Systems.XLSX

Hydroponic and aquaponic farming is becoming increasingly popular as a solution to address global food security. Plants in hydroponic systems are grown hydroponically under controlled environments and are considered to have fewer food safety concerns than traditional field farming. However, hydroponics and aquaponics might have very different sources of microbial food safety risks that remain under-examined. In this study, we investigated the microbiomes, microbial hazards, and potential bacterial transmission routes inside two commercial hydroponic and aquaponic farming systems using 16S-ITS-23S rRNA sequencing and a hydroponic food safety practice survey. The hydroponic farming system microbiome was analyzed from the fresh produce, nutrient solution, tools, and farmworkers. Proteobacteria, Actinobacteria, Cyanobacteria, Bacteroidetes, and Firmicutes were the main components of hydroponic/aquaponic farming systems, with Pseudomonas being the most abundant genus in fresh produce samples. We further identified the presence of multiple spoilage bacteria and potential human, plant, and fish pathogens at the subspecies level. Spoilage Pseudomonas spp. and spoilage Clostridium spp. were abundant in the hydroponic microgreen farm and aquaponic lettuce farm, respectively. Moreover, we demonstrated the mapping of Escherichia coli 16s-ITS-23s rRNA sequence reads (∼2,500 bp) to small or large subunit rRNA databases and whole-genome databases to confirm pathogenicity and showed the potential of using 16s-ITS-23s rRNA sequencing for pathogen identification. With the SourceTracker and overlapping amplicon sequence variants, we predicted the bidirectional transmission route between plants and the surrounding environment and constructed the bacteria transmission map, which can be implemented in future food safety risk control plans.

水培与鱼菜共生农业作为解决全球粮食安全问题的可行方案，正日益受到广泛青睐。水培系统中的作物均在可控环境下以水培方式栽培，相较于传统大田种植，其食品安全隐患相对更低。然而，水培与鱼菜共生体系可能存在截然不同的微生物食品安全风险来源，且此类风险尚未得到充分研究。本研究依托16S-ITS-23S核糖体RNA（rRNA）测序技术与水培食品安全实践调查问卷，对两套商业化水培及鱼菜共生农业系统内的微生物组、微生物危害及潜在细菌传播路径展开了系统性调研。研究人员从新鲜农产品、营养液、作业工具及农场从业人员四个采样维度，对水培农业系统的微生物组进行解析。变形菌门（Proteobacteria）、放线菌门（Actinobacteria）、蓝细菌门（Cyanobacteria）、拟杆菌门（Bacteroidetes）及厚壁菌门（Firmicutes）为水培/鱼菜共生农业系统的核心微生物类群，其中假单胞菌属（Pseudomonas）在新鲜农产品样本中丰度最高。本研究进一步在亚种水平上鉴定出多种腐败菌，以及潜在的人类、植物与鱼类病原体。水培微型蔬菜农场与鱼菜共生生菜农场中，分别以腐败假单胞菌属（Pseudomonas spp.）与腐败梭菌属（Clostridium spp.）为优势类群。此外，本研究通过将大肠杆菌（Escherichia coli）的16S-ITS-23S rRNA序列读长（约2500 bp）比对至小亚基或大亚基rRNA数据库及全基因组数据库以验证其致病性，同时证实了利用16S-ITS-23S rRNA测序技术进行病原体鉴定的应用潜力。本研究借助源追踪分析工具（SourceTracker）与重叠扩增子序列变异体，预测了作物与周边环境之间的双向细菌传播路径，并构建了细菌传播图谱，可用于后续食品安全风险防控方案的制定与实施。